LAMMPS (4 Feb 2020)
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors
  special bonds CPU = 0.00095129 secs
  read_data CPU = 0.0199838 secs

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp  275.0 275.0 100.0 tchain 1

fix		2 all plumed plumedfile plumed.dat outfile p.log
fix		2a ref setforce 0.0 0.0 0.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles
  find clusters CPU = 0.000829935 secs

#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2
thermo		10
variable        step equal step
variable        pe equal pe

run		101
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
SHAKE stats (type/ave/delta) on step 0
  4 1.111 1.44264e-05
  6 0.996998 7.26967e-06
  8 1.08 1.32536e-05
  10 1.111 1.22749e-05
  12 1.08 1.11767e-05
  14 0.96 0
  18 0.957206 4.37979e-05
  31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.23 | 16.42 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152            0 
      10     276.9783   -5234.3057   -6348.6171    1114.3114   -6421.6171    17.024361   0.47785504 
      20    279.08532   -5226.4036   -6349.1917    1122.7881   -6441.0169    20.764378   0.52605302 
      30    282.32141   -5222.3866   -6358.1939    1135.8073   -6448.9785    22.945165   0.65106011 
      40    276.34173   -5218.7623   -6330.5128    1111.7504   -6423.7566    15.655345   0.23795099 
      50    286.12741   -5215.9248   -6367.0439    1151.1192   -6449.2655    17.420975   0.42646205 
      60    273.01449   -5217.7381   -6316.1026    1098.3646   -6406.4709    21.800931   0.92327815 
      70    274.67549   -5221.0246   -6326.0716     1105.047   -6409.7721     19.41235 0.0016975896 
      80    273.74824   -5224.7613   -6326.0778    1101.3165   -6418.5055    19.206793   0.48550348 
      90    284.32594    -5229.195   -6373.0667    1143.8717   -6461.3467    21.124789    0.5468014 
SHAKE stats (type/ave/delta) on step 100
  4 1.111 2.06868e-06
  6 0.996999 2.09521e-06
  8 1.08 1.10835e-06
  10 1.111 2.46599e-06
  12 1.08 8.86314e-07
  14 0.959999 0
  18 0.9572 9.14098e-06
  31 104.52 0.000760401
     100    270.40648   -5234.9604   -6322.8327    1087.8723     -6417.73    19.666404 0.0094784372 
     101    270.99811   -5235.8295    -6326.082    1090.2525   -6418.8974    17.285816  0.086681332 
Loop time of 0.873215 on 4 procs for 101 steps with 2004 atoms

Performance: 19.987 ns/day, 1.201 hours/ns, 115.664 timesteps/s
92.5% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.58191    | 0.61681    | 0.66371    |   3.8 | 70.64
Bond    | 0.00099587 | 0.0023546  | 0.0041356  |   2.8 |  0.27
Kspace  | 0.096162   | 0.14486    | 0.18119    |   8.1 | 16.59
Neigh   | 0.059843   | 0.059864   | 0.059876   |   0.0 |  6.86
Comm    | 0.013623   | 0.01368    | 0.013723   |   0.0 |  1.57
Output  | 0.00031137 | 0.0010193  | 0.0024326  |   2.6 |  0.12
Modify  | 0.031552   | 0.031697   | 0.032087   |   0.1 |  3.63
Other   |            | 0.002938   |            |       |  0.34

Nlocal:    501 ave 512 max 492 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost:    6570.25 ave 6604 max 6529 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs:    176990 ave 181122 max 173551 min
Histogram: 1 1 0 0 0 0 1 0 0 1

Total # of neighbors = 707961
Ave neighs/atom = 353.274
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:00
